IPX had become aware of the distant world following an incident on Mars in 2253[2] Following the last war the Shadows had dispersed their ships across the galaxy, seeding them on distant world as a precaution to keep their forces intact while they slept. One of these had been left behind on Mars and was detected by an IPX team lead by a Dr. Mary Kirkish. The xenoarchaeologists were eventually ordered to pull back and watched as unmarked shuttles belonging to the Psi Corps's Department Sigma took over the dig.[3] Working quickly, knowing that it had started to transmit a homing signal once exposed, they managed to obtain samples and implant a homing beacon of their own before another identical Shadow ship arrived, digging the first ship out of the ground and activating it. The two then returning to Z'ha'dum.[2][3][4]

"...the Icarus. They found something?"

In 2256 IPX, under contract from the Earthforce New Technologies Division, sent the science vessel Icarus to follow it and investigate, arriving at Z'ha'dum in January 2257.[5] The recently awakened Shadows captured the crew shortly after they landed and offered the crew a chance to serve them. Those who refused —including Anna Sheridan — were turned into "CPUs" for the Shadow ships. Some small part of the crew did agree to serve the Shadows, including Mr. Morden. At the same time that the Shadows started to 'awaken', the Vorlons began to prepare for the coming war as well. Secretly, they made contact with the leader of the MinbariGrey Council, Dukhat, knowing that the humans were "the key" to this cycle of the great conflict with their nemesis. While it is possible (or even probable) that their interactions led to the Earth-Minbari War, it also indirectly led to the construction of both Babylon stations 4 and 5, critical for the previous and coming wars, respectively. The Minbari Anla'Shok — frowned upon as something of a joke by the Minbari Warrior Caste — continued to hold their faith in Valen's prophecies that the Shadows would soon return as the hour drew close, starting their own preparations.[1][2]

The first known direct act by the Shadows (or their agents) came in 2254, when a series of Shadow Fighters attempted to plant a large fusion bomb on Babylon 4 in an attempt to destroy it, setting up an alternate timeline where without Valen and the station, the Shadows would come out of the last war far stronger losers, able to move much faster and harder, allowing in the destruction of Babylon 5 at the end of 2260. This attempt was foiled by the White Star 1, which came back in time from 2260, completing the time loop that sent both Babylon 4 and Valen back in time to win the last Shadow War.[6]

Mr Morden served as the primary spokesman for the Shadows

In 2258, the Shadows made their first known indirect moves at interacting with the major Galactic powers, with Mr. Morden arriving on the Station as a representative of the Shadows, though he took great pains to only ever refer to the Shadows as his "associates", leaving the identity of his backers a mystery. To this end, Morden visited the various alien Ambassadors and asked them the Shadows' infamous question: "What do you want?".
Delenn, sensing the presence of the Shadows around him sent Morden away abruptly, taking his presence as a sign to begin her own preparations for the coming war, regardless of what the Grey Council thought. G'Kar, lacking a vision beyond simple revenge upon the Centauri, did not impress Morden or his "associates". Londo however, who dreamed of the Centauri becoming strong once again, regaining their power and place across the Galaxy, did. Morden and his Shadow minders were also briefly confronted by Kosh on this first visit to Babylon 5, but given the "rules" between the Vorlons and the Shadows, it would appear that there were few real consequences to a short standoff between them, during which the Vorlon warned the Shadows that "they are not for you".[7]

The White Star Fleet was completed shortly before major fleet actions against the Shadows

The Shadows, however, did not back off, instead forging a strong alliance of convenience with Londo, doing him favors for no apparent price that caused his stature to rise dramatically back home.[7][8] At the same time — probably from their interactions with Morden and the Icarus crew — the Shadows took a great deal of interest in humanity, having Morden establish a far more open dialog with certain factions in Earth including Morgan Clark and part of the Psi Corps,[9] leading to the assassination of President Santiago and ascension of Clark to the Presidency of the Earth Alliance.[10] By 2259 Earthforce had secretly built Shadow hybrid vessels, prototypes for merging Shadow and human warship technology.[11][12]

By early 2259, the Rangers had also began to prepare in earnest for the Shadow War with the help of the Vorlons, including commissioning of a line of new White Star class warships without the knowledge of the Warrior Caste or most of the Grey Council. Jeffrey Sinclair was recalled from Babylon 5 to take up a post as the Earth Alliance Ambassador to Minbar; but without the knowledge of EarthGov, the Grey Council made him the leader of the Rangers. Humans also were allowed to join the Rangers as equals, welcomed freely by the Minbari members who did not resign from the order, though the idea was not supported by most Minbari Warriors.[13]

"August 3, 2260. Personal diary. Ten days ago, for the first time, the Shadows began attacking openly"

– Commander Susan Ivanova

The Shadows early on appeared content to provide a supporting role behind the scenes, helping their "friends" — such as Mollari — without them realizing just who they had allied themselves with. Nonetheless, their machinations soon resulted in accelerated events such as the Earth Alliance turning into a totalitarian state, the Narn declaring war against the Centauri, the Centauri expanding and fighting manyLeague of Non-Aligned Worlds races, and the League worlds then turning on each other at the Shadows encouragement [14]; all of these things dedicated to their goal of encouraging Strength through Chaos.[2] Occasionally their forces would make direct appearances, such as their destruction of the Narn Fleet in the Battle of Gorash VII[15], but mostly the Shadows worked from behind the scenes.

The Vorlons engage the Shadows directly for the only time prior to their final battle, solidifying the Army of Light

At the same time, the 'Army of Light' was taking its first steps. Draal, the custodian of the Great Machine on Epsilon 3, put his resources at the disposal of Sheridan and Delenn [15], who also started to use the Rangers to investigate the actions and influence of the Shadows, while buying time to gather strength and prepare for the war. The Shadows, seeing the Rangers as a direct threat attempted to take direct action against them on at least one occasion, but failed.[9]
Shortly after the breakaway of Babylon 5 from the Earth Alliance, the Shadows started to move openly, displaying their ships and power as they struck almost randomly at the League, bringing chaos to their already depleted forces in their goal to let the worthy survive and the weak perish. The Babylon 5's command staff and the Ranger/Minbari backbone worked to unite the League against the Shadows, unsuccessfully until the Vorlons directly intervened and destroyed a Shadow fleet at Sheridan's insistence. This apparent violation of the "rules" between the Shadows and Vorlons led to swift retaliation with the assassination of Kosh by Morden's Shadow associates, which appeared to restore the status quo between the two sides. Yet Kosh' death was not in vain: seeing that — apparently — Babylon 5 had allies just as strong as the Shadows, the League rallied into the Army of Light, allying together to face the Darkness.[16]

'Break and attack!' The Army Of Light engages the Shadows in 'Shadow Dancing', defeating them for the first time

At this time, the causality loop of Babylon 4 returning to the past was completed by the Babylon 5 crew, who jumped back in time six years to make the events happen 'as they were supposed to happen'. Jeffrey Sinclair, the Entil'Zha of the Rangers, took Babylon 4 back 1000 years with Draal and Zathras' help. After arriving in the past, he used the technology Delenn had used to become half human to make himself fully Minbari in appearance. He became Valen, the legendary leader who would defeat the Shadows and establish the Anla'Shok and the Grey Council.[17] After Sinclair departed, Delenn became Entil'Zha of the Anla'Shok and alongside Sheridan, one of the two major leaders of the Army of Light against the Shadows.[18]

This Army of Light, after discovering the vulnerability of Shadow ships to telepathic jamming, launched a major fleet action against the Shadows, combining large elements of the various allied fleets, telepathic attacks and well-developed intelligence to successfully defeat a major Shadow force in a direct engagement. While the Army of Light lost ships at a ratio of 2:1 to achieve this victory, it was a victory nonetheless: the Shadows were forced to retreat and had been delivered a message that their attempt to spread disorder and chaos was failing.[19] The Shadows reacted by sending John Sheridan's wife, Anna, who had been enslaved and brainwashed by the Shadows after refusing to serve them, to invite him to Z'ha'dum to hear "their side of the story" of the conflict between them and the Vorlons, in the hope of convincing him of the rightness of their side. Knowing it was almost certainly a trap, but afraid from a vision of the future that not going to Z'ha'dum would cause even more problems, John left with Anna on the White Star 1. After speaking with the Shadows' representatives, Sheridan rejected their position and fought his way clear. Hopelessly cut off on the Shadows' homeworld, he chose to take his life by detonating two 500 Megaton fusion bombs on the White Star, destroying a major Shadow city while leaping to his apparent death — and opening a door for the war to enter a new and unexpected direction.[2]

The Vorlons take advantage of the opportunity created by Sheridan's 'death' at Z'ha'dum to deploy their Planet Killer...

Sheridan's actions on Z'ha'dum delivered a stunning blow to the Shadows, but they were almost in vain. In the aftermath of his "death", the Army of Light started to fracture. Encouraged by the lack of any Shadow reprisals in the aftermath of Z'ha'dum, some League races concluded that the war had indeed ended. Despite the belief of key figures such as Delenn that the war was far from over, certain members of the League, such as the Drazi, started to push to breakup the Army of Light, under the assumption that keeping it in force would only incite the Shadows to strike back instead of vanishing again for another thousand years.[20]

Delenn however was undeterred by their push and started to gather the still loyal forces of the Army of Light for a final strike before their strength was too diluted to have even a slim hope against their enemy.[21][22] Alarmed by actions they believed would only restart the war, those opposed attempted to publicly depose her, only to be dramatically put down by the return of a very much alive John Sheridan, who finally understood the reasons behind the war. He quickly sought to gather an alliance of the Younger Races never before seen to end the cycle once and for all.[22]

...And the Shadows retaliate with their own Planet Killer

At the same time however, Sheridan's attack on Z'ha'dum opened a new phase of the war that no one expected. In the aftermath of his attack, the Shadows took precaution of dispersing their fleets to numerous staging points across the Galaxy, to prevent any other such "sneak attacks" from causing major damage to their forces as they licked their wounds. In some cases, such as Centauri Prime, the Shadows were welcomed openly by the Government [20]; whereas others, such as Coriana VI, lacked the means to fight back and therefore simply gave in to their presence.[23]

Unfortunately for those planets, being so openly touched by the Shadows, at least in the minds of the Vorlons, meant they had become irreparably tainted by the "disease", regardless of whether the worlds could have possibly refused the "request" to host a fleet of Shadow vessels. Now that Sheridan had broken the rules by using weapons of mass destruction direction on the Shadow planet, the Vorlons felt freed to use their own weapons of mass destruction.[23] The Vorlon fleet swung into action on a scale not seen for at least a thousand years. They deployed Vorlon planetkillers, which first destroyed a Shadow base on the planet Arcata VII[22], and then destroyedVentauri III[24], followed byTazino Prime and several other inhabited planets. In response to this dramatic escalation, the Shadows swiftly deployed their own Planet Killers, destroying a colony on the edge of Vorlon space, restarting the war at a terrifying new level as the two First Ones worked to exterminate any species who supported their other side, the logical outcome of which could only be the genocide of most of the Younger races across the Galaxy.[25]

"A brilliant strategy. He's making a crucible which he hopes will force out the truth. Quite brave. Possibly futile... but very human"

– Lorien

Understanding had finally come to the Younger Races. For the first time since the cycle of conflict between the Vorlons and Shadows had started, the truth of the First Ones' goals and motives had been laid bare to the Younger Races thanks to Sheridan's adventure on Z'Ha'Dum. Both the Vorlons and Shadows had stayed behind when the other First Ones had moved beyond the Rim as shepherds and guardians of the Younger Races. Their purpose had been to teach until they were ready to stand on their own, and then to step aside, much as Lorien had done for them so long ago. But over time, these once noble ideals had started to slip away as guidance turned into manipulation, and teaching into indoctrination. Convinced that their answer was the only answer, both the Vorlons and Shadows had spent untold millennia manipulating the Younger races as proxies for the 'great argument', no longer for any benefit of the Younger races, but simply to prove that 'they' had been right all along. And now not even that was enough, as both sides deployed their Planet Killers in an attempt to wipe out anyone following the message of the other side.[23] The targets had been small at first, but Ranger scout ships had located the Vorlon fleets moving through hyperspace and determined their next targets. In six days, both Coriana IV and Centauri Prime would be destroyed by Vorlon Fleets led by planet killers, slaughtering populations of six and three billion respectively.

"So what are you going to do, Mollari? Huh? Blow up the island?"

Knowing they had only sufficient ships to make a stand in one system, Sheriden chose Coriana VI on the basis of population size, twice that of Centauri Prime. However he did send a warning to Londo about the Vorlon threat who soon found himself forced to move against Emperor Cartagia, when it became clear that far from taking action to expel any Shadow influence that would bring down the Vorlons wrath, the insane monarch wanted to let the Vorlons destroy the Centuari homeworld. He welcomed it as the event that would propel him into Godhood. In horror, Londo moved swiftly, forming an alliance with G'Kar and other Centauri nobles to depose the Emperor and reverse his policies regarding the Shadows. Although time was short, they successfully assassinated the Monarch and took control of the Government, starting a frantic and ruthless purge of any trace of Shadow influence on Centuari prime, freeing Narn as the price for G'Kar's help, racing against the clock of the Vorlons' arrival.[24] The Shadow fleet stationed on the planet was simply blown up along with the entire island they were based on using smuggled fusion bombs. Meanwhile Morden and his Shadow advisers were executed on the direct orders of Londo, now Prime Minister and de-facto leader of the Republic during the time of crisis.[23]

Simultaneously, the Army of Light made its own preparations, gathering its full strength to make their stand at Coriana VI. However Sheridan did not simply wish to hold the line against the Vorlons; he wanted to seize the unique chance to end the cycle of proxy wars between the Vorlons and Shadows once and for all. To that end, he devised a plan to bring the Shadows into the same battlefield. As the two First Ones had been carefully avoiding each other, his only option was to trick the Shadows to the same battlefield. He gave White Star 14, under Shok-naEricsson, orders to lead an attack against a Shadow base on Dorak VII. His White Star would be carrying falsified data on a top-secret staging ground the Army of Light was preparing on Coriana VI that could not be allowed to fall into Shadow hands during this attack... however his mission orders were to ensure, with the deaths of his crew, his ship, and himself, that this data would fall into Shadow hands, and to make it look like the Rangers had fought to the death to protect this information. As was their creed, the Rangers did their duty and Died for The One. The Shadows took the bait and sent their own fleet and Planet Killer hurtling towards Coriana VI in an attempt to wipe out the gathered fleet the data said would be waiting, while the Vorlons and Army of light also converged in the greatest single naval engagement in recent history.[25]

"Not bad. We still can't win, but it's not bad."
"We can't win? "
"Against the Vorlons AND the Shadows? No"
"Then what are we doing here?"
"Hoping that the truth will set us free!"

– Sheriden and Marcus

The Army of Light awaits the First Ones in orbit of Coriana VI

The Vorlon and Shadow fleets arrived simultaneously. Both sides at once saw the other, jumped to the perfectly natural conclusion that the 'rules' had been thrown out the window. Completely ignoring the massed fleets of the Army of Light, the First Ones charged straight for each other. They were rather abruptly reminded of the Younger Races however, when with the same tactic that had destroyed the Black Star, Sheridan detonated a number of fusion bombs hidden on asteroids in and around the Shadow and Vorlon fleets. He destroyed and damaged several ships on both sides and, in the words of Lyta Alexander, "pissed" them off.

Promptly a three way battle, the final battle of the Second Shadow War commenced. Attempts to communicate with the Vorlons and plead with them to spare Coriana VI as being utterly unable to prevent the Shadows from landing were simply ignored and, despite the three-way battle that raged on, the Vorlons managed to push their Planet Killer into range of Coriana VI. Unwilling to sit back and let them die, Sheridan called in his final ace in the hole; the remaining First Ones from across the Galaxy. Having answered Lorien's call to battle, the First Ones jumped into the fray and directed their wraith at the Vorlon Planet Killer, destroying it in a matter of seconds before they sided with the Younger Races against their peers, destroying Shadow and Vorlon alike.

The Vorlon Planet killer dies at the hands of the remaining First Ones.

Back on Centauri prime, the expected Vorlons also arrived. Londo, believing he had saved his world by destroying anything touched or influenced by the Shadows, then damned it unintentionally by showing himself - quite possibly the single greatest influence of the Shadows on his people - to be alive and well when he sent a message to the Vorlons saying what they had done. Consequently as the Vorlons swept the planetary defenses aside and prepared to fire their Planet Killer, Londo frantically demanded that Vir kill him and show the Vorlons the proof, that being the only way their hand could be stayed. But that proved unnecessary as the Vorlons suddenly left, called to Coriana VI to reinforce the fleet there which had just lost its planet killer at the hands of the other First Ones.

After the Vorlon Planet Killer's destruction by the other First Ones, the Vorlons and Shadows both stepped back from the combat, realizing events had firmly moved beyond their control. Finally deigning to respond to the Younger Races' attempts to talk to them, the Vorlons and Shadows jointly seized control of Lyta, using her in turn to snare both Sheridan and Delenn into a private telepathic link. The Vorlons tried to convince Sheridan of the rightness of their cause, and the Shadows attempted to prove to Delenn their own position was superior. However, unknown to both sides, Lorien himself stepped in at this point, working to show all those in the fleet everything as it happened. Chided and furious that 'the game' was up, the Shadows made one last play, moving their Death Cloud around the Army of Light fleet and trapping them, demanding one last time that they make a choice between Order and Chaos.

"Who are YOU? What do YOU want?"

Sheridan and Delenn however rejected the choice itself, refusing to take sides anymore. They declared that from now on the Younger Races would find their own way between Order and Chaos, between Darkness and Light. A final attempt to 'kill the message' by firing Death Cloud missiles at the White Star 2 was thwarted when the rest of the Army of Light fleet moved in, taking the hits in their place, proving to everyone that the Younger Races collectively rejected the Vorlon and Shadow positions. Finally, Lorien himself stepped in and gently told his 'children' that their time had finally come. The Younger Races had clearly learned to stand on their own, and the shepherds' presence was no longer necessary, wanted, or warranted. It was time for all the remaining First Ones to move beyond the Rim, to now leave the Galaxy and truly let the Younger Races grow without interference or manipulation.

And with that, Lorien led the Vorlons, the Shadows and the other First Ones who had come to the battle beyond the Rim, ending the Second age and starting a new Third Age, where the Young races of the Galaxy would now stand or fall on their own.[23]

The end of the Second Shadow war ended the manipulation of the Younger Races by the vastly older First Ones, allowing them to stand and fall entirely on their own actions and choices.[23] However the legacy of the Vorlon and Shadow conflict would be felt for a very long time to come. While the First Ones left, vast amounts of their technology remained that was eagerly seized and used by various powers. Shadow Technology especially became a recurring nightmare for the Milky Way over the next decade, often in the hands of the Shadows' favored servants, the Drakh, who now lacking their Masters' guidance would attempt to become Masters of Chaos themselves.[26][27]

The Vorlons too left much behind that would cause problems. The Thirdspace jumpgate, the Vorlons' "greatest mistake," would be rediscovered and come perilously close to spelling utter annihilation for the Younger Races [28]. The Vorlon homeworld was put off-limits for a million years, until the Younger Races were "ready".[26]